Human parasites cause some of the most important infectious diseases worldwide (e.g. malaria), and infect millions of individuals each year within the US (e.g. toxoplasma). Despite the availability of several reference sequences for parasite genomes, we have a very limited understanding of the mechanisms by which parasites infect and persist within their human hosts. This project will exploit current high-throughput sequencing technologies and bioinformatics techniques to provide novel insights to parasitic infectious diseases. Our broad objectives are to understand pathogen diversity, evolution, and their interactions with the human host and associated microbiota. These objectives are addressed through three specific aims, applied to two apicomplexan species of major concern in the US {Toxoplasma gondii) and worldwide {Plasmodium falciparum). Particular emphasis is given to the study of host-parasite interactions, through the sequencing of DNA and RNA from both the parasites and their human hosts. Specific Aim 1 will apply sequence-based analysis of natural and mutant T. gondii strains to determine the worldwide genomic complexity for this species, and permit predictions of host and parasite genes that are involved with specific infection and replication phenotypes. Specific Aim 2 will apply sequence-based analysis of host-parasite interactions during experimental and natural P. falciparum infections of humans, to identify the genomic and transcriptomic basis of immune profiles that are associated with protection from the symptoms of malaria. Specific Aim 3 will characterize the composition of bacterial and eukaryotic species in the gut microbiome during the course of infections with P. falciparum to determine the reciprocal effects on microbiome composition and disease progression. Each of the specific aims employs innovative experimental designs and technology development, and is most appropriate for a large-scale program that can generate and process extensive volumes of sequence data. The project addresses important problems that apply to the specific species under study, and to the larger field of parasitic infectious disease. By achieving the objectives of this project, we will provide a model for how future projects could be accomplished for many other pathogens of interest.